Informative genomic microsatellite markers for efficient genotyping applications in sugarcane.
Genomic microsatellite markers are capable of revealing high degree of polymorphism. Sugarcane (Saccharum sp.), having a complex polyploid genome requires more number of such informative markers for various applications in genetics and breeding. With the objective of generating a large set of microsatellite markers designated as Sugarcane Enriched Genomic MicroSatellite (SEGMS), 6,318 clones from genomic libraries of two hybrid sugarcane cultivars enriched with 18 different microsatellite repeat-motifs were sequenced to generate 4.16 Mb high-quality sequences. Microsatellites were identified in 1,261 of the 5,742 non-redundant clones that accounted for 22% enrichment of the libraries. Retro-transposon association was observed for 23.1% of the identified microsatellites. The utility of the microsatellite containing genomic sequences were demonstrated by higher primer designing potential (90%) and PCR amplification efficiency (87.4%). A total of 1,315 markers including 567 class I microsatellite markers were designed and placed in the public domain for unrestricted use. The level of polymorphism detected by these markers among sugarcane species, genera, and varieties was 88.6%, while cross-transferability rate was 93.2% within Saccharum complex and 25% to cereals. Cloning and sequencing of size variant amplicons revealed that the variation in the number of repeat-units was the main source of SEGMS fragment length polymorphism. High level of polymorphism and wide range of genetic diversity (0.16-0.82 with an average of 0.44) assayed with the SEGMS markers suggested their usefulness in various genotyping applications in sugarcane.
Parida
Swarup K
SK
National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110012, India.
Kalia
Sanjay K
SK
Kaul
Sunita
S
Dalal
Vivek
V
Hemaprabha
G
G
Selvi
Athiappan
A
Pandit
Awadhesh
A
Singh
Archana
A
Gaikwad
Kishor
K
Sharma
Tilak R
TR
Srivastava
Prem Shankar
PS
Singh
Nagendra K
NK
Mohapatra
Trilochan
T
D001483:Base Sequence; D005819:Genetic Markers; D015698:Genomic Library; D005838:Genotype; D018895:Microsatellite Repeats; D008969:Molecular Sequence Data; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D011110:Polymorphism, Genetic; D031786:Saccharum / Q000235:genetics*; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000379:methods
D005819:Genetic Markers